Exploration of Enzyme Diversity by Integrating Bioinformatics with

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Exploration of enzyme diversity by integrating bioinformatics with expression analysis and biochemical characterization Pavel Vanacek, Eva Sebestova, Petra Babkova, Sarka Bidmanova, Lukas Daniel, Pavel Dvorak, Veronika Stepankova, Radka Chaloupkova, Jan Brezovsky, Zbynek Prokop, and Jiri Damborsky ACS Catal., Just Accepted Manuscript • DOI: 10.1021/acscatal.7b03523 • Publication Date (Web): 02 Feb 2018 Downloaded from http://pubs.acs.org on February 4, 2018

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ACS Catalysis

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Exploration of enzyme diversity by integrating bioinformatics

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with expression analysis and biochemical characterization

3

Pavel Vanacek1,2#, Eva Sebestova1#, Petra Babkova1,2, Sarka Bidmanova1,2, Lukas Daniel1,2,

4

Pavel Dvorak1, Veronika Stepankova1,2,3, Radka Chaloupkova1,2,3, Jan Brezovsky1,2, Zbynek

5

Prokop1,2,3*, Jiri Damborsky1,2*

6 7

Affiliations

8

1

9

Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University,

Loschmidt Laboratories, Department of Experimental Biology and Research Centre for

10

625 00 Brno, Czech Republic

11

2

12

Brno, Czech Republic

13

3

International Clinical Research Center, St. Anne's University Hospital, Pekarska 53, 656 91

Enantis Ltd., Biotechnology Incubator INBIT, Kamenice 34, 625 00 Brno, Czech Republic

14 15

#

authors

contributed

equally;

*

authors

for

correspondence:

Zbynek

Prokop,

16

[email protected], phone +420-5-4949-6667; Jiri Damborsky, [email protected],

17

phone +420-5-4949-3467

18

1 ACS Paragon Plus Environment

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Abstract

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Millions of protein sequences are being discovered at an incredible pace, representing an inexhaustible

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source of biocatalysts. Here, we describe an integrated system for automated in silico screening and

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systematic characterization of diverse family members. The workflow consists of: (i) identification

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and computational characterization of relevant genes by sequence/structural bioinformatics, (ii)

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expression

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biochemical/biophysical characterization, was validated against the haloalkane dehalogenase family.

26

The sequence-based search identified 658 potential dehalogenases. The subsequent structural

27

bioinformatics prioritized and selected 20 candidates for exploration of protein functional diversity.

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Out of these twenty, the expression analysis and the robotic screening of enzymatic activity provided 8

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soluble proteins with dehalogenase activity. The enzymes discovered originated from genetically

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unrelated Bacteria, Eukaryota, and also Archaea. Overall, the integrated system provided biocatalysts

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with broad catalytic diversity showing unique substrate specificity profiles, covering a wide range of

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optimal operational temperature from 20 to 70 °C and an unusually broad pH range from 5.7 to 10. We

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obtained the most catalytically proficient native haloalkane dehalogenase enzyme to date (kcat/K0.5 =

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96.8 mM-1.s-1), the most thermostable enzyme with melting temperature 71o C, three different cold-

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adapted enzymes showing dehalogenase activity at near-to-zero temperatures and a biocatalyst

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degrading the warfare chemical sulfur mustard. The established strategy can be adapted to other

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enzyme families for exploration of their biocatalytic diversity in a large sequence space continuously

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growing due to the use of next-generation sequencing technologies.

analysis

and

activity

screening

of

selected

proteins,

and

(iii)

complete

39 40 41 42 43 44

Keywords

45

Diversity, sequence space, bioinformatics, biocatalyst, biochemical characterization, activity, substrate

46

specificity, haloalkane dehalogenases


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Introduction

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The post-genomic era is characterized by an exponential increase in the number of protein

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sequences1, which represent an immense treasure of novel enzyme catalysts with unexplored

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structural-functional diversity. Despite their enormous promise for biological and biotechnological

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discovery, experimental characterization has been performed on only a small fraction of the available

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sequences2. This ‘big data‘ problem is further extended by continuous genome and metagenome

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sequencing projects which employ powerful next-generation sequencing technologies3,4. Traditional

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biochemical techniques are time-demanding, cost-ineffective and low-throughput, providing

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insufficient capacity for the exploitation of genetic diversity5. In response to these limitations, high-

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throughput experimental techniques employing miniaturisation and automation have been developed

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in order to keep track of the ever-growing sequence information6–8. Although fluorescent biochemical

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assays implemented in micro-formats provide easily-measurable signals, enzyme activities from

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determined endpoint measurements often differ from those obtained using native substrates (“You get

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what you screen for”)6. These micro-format techniques are powerful tools for the pre-filtering of large

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libraries; however, they must be followed by additional assays with the target substrates. Robotic

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platforms using the microtiter plate format are therefore employed to provide quantitative kinetic

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data9. Despite these innovations, the existing experimental methods do not provide sufficient capacity

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for the full biochemical/biophysical characterization of proteins spanning the ever-increasing sequence

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space, and new technical solutions are therefore required.

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Computational approaches offer an adequate capacity for in silico screening of a large pool of

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sequence entries to facilitate the identification and rational selection of attractive targets for

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experimental testing. The recently published genomic mining strategy employing molecular modelling

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and structural bioinformatics has demonstrated the identification of enzymes catalysing the targeted

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reaction in a synthetic pathway. This exciting approach led to the discovery of decarboxylases from

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more than 239 selected hits without expensive and laborious enzyme-engineering efforts10. The main

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benefit of this study lies in the effective sampling of particular enzymatic activity from sequence

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databases. Developing automated computational workflows and integrating them with experimental

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platforms is thus essential if the effective discovery of novel proteins is desired. In addition to their

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applicability in finding new members of protein families, they can identify a wealth of functional

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novelty when a homolog is found in an unexpected biological setting (such as a new species or

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environment) or co-occurring with other proteins11. Likely hotspots of functional novelty in sequence

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space may be uncovered either in under-sampled phyla from the tree of life or by finding functional

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shifts in sequence motifs or domain architecture12. Moreover, in silico analysis of structural and

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functional properties can reveal evolutionary changes in the enzymatic machinery.


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Here we describe an integrated system comprising automated in silico screening protocol and

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experimental procedures for characterisation and the exploitation of the structural and functional

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diversity of an entire enzyme family (Figure 1). As proof of concept, we used this system to explore

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the diversity of microbial enzymes haloalkane dehalogenases (EC 3.8.1.5, HLDs). HLDs have been

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identified in a broad spectrum of microorganisms inhabiting soil, water, animal tissues and symbiotic

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plants13–21. These α/β-hydrolase fold enzymes, which belong to one of the largest protein superfamilies

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(>100.000 members), catalyze the hydrolytic dehalogenation of a wide range of organohalogens.

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HLDs can be employed for the biocatalysis of optically pure building blocks22–24; the bioremediation

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of environmental pollutants25–27; the decontamination of chemical warfare agents28,29; the biosensing of

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pollutants30–32; and molecular imaging33–35. This diversity of reported practical applications is

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especially astonishing if one bears in mind that only two dozen HLDs have been biochemically

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characterized during the last thirty years, although the sequences of hundreds of putative HLDs are

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available in genomic databases20,36. The proposed integrated system effectively explored the sequence

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diversity and delivered eight novel biocatalyst possessing unique properties. Particularly, the most

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catalytically proficient HLD enzyme to date, the most thermostable variant and the extremophile-

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derived enzymes are promising for various biotechnological applications. The strategy was critically

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evaluated by validation of in silico predictions against experimentally verified results.

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Experimental section

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In silico screening

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The sequences of three experimentally characterized HLDs were used as queries for two

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iterations of PSI-BLAST v2.2.28+37 searches against the NCBI nr database (version 25-9-2013)38 with

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E-value thresholds of 10-20. Information about the source organisms of all putative HLDs was

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collected from the NCBI Taxonomy and Bioproject databases38. A multiple sequence alignment of all

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putative full-length HLD sequences was constructed by Clustal Omega v1.2.039. The homology

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modelling was performed using Modeller v9.1140. Pockets in each homology model were calculated

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and measured using the CASTp program41,42 with a probe radius of 1.4 Å. The CAVER v. 3.01

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program43 was then used to calculate tunnels in the ensemble of all homology models. The three-

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dimensional structures of 34 halogenated compounds, which are environmental pollutants, artificial

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sweeteners, chemical warfare agents or their surrogates and disinfectants, were constructed in

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Avogadro44 and docked to the catalytic pockets using AutoDock 4.2.3. Each local search was based on

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the pseudo Solis and Wets algorithm with a maximum of 300 iterations per search45. The chance for

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soluble expression in E. coli of each protein was predicted based on the revised Wilkinson-Harrison

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solubility model46,47. Detailed bioinformatics protocols are described in the Supporting Information.


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Figure 1. Workflow of an integrated system for the exploitation of the protein structural and

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functional diversity. Different colours highlight three distinct phases of the workflow: (i) automated

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sequence and structural bioinformatics (green), (ii) protein production and robotic activity screening

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(blue) and (iii) biochemical characterization (red). The timeline shows the periods required for data

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collection and analysis, divided into intervals of 4 hours, 4 days, 3 weeks and 3 months column for

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clarity.

A

cut

square

indicates

a

time

requirement

of

less

than

one

hour.


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Expression analysis and activity screening

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Codon-optimized genes encoding 20 putative HLDs were designed and commercially

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synthesized. The synthetic genes were subcloned individually into the expression vector pET21b

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between the NdeI/XhoI restriction sites. E. coli BL21(DE3), E. coli ArcticExpress(DE3), and E. coli

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Rosetta-gami B(DE3) pLysS competent cells were transformed with DNA constructs using the heat-

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shock method and expressed in lysogeny broth (LB) or Enbase medium. Biomass was harvested at the

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end of the cultivation, washed and disrupted using a homogenizer. The activity of cell-free extract

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towards 1-iodobutane, 1,2-dibromoethane, and 4-bromobutyronitrile substrates was robotically

129

screened at 10, 37 and 55 °C. Detailed experimental protocols are described in the Supporting

130

Information.

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Biochemical and biophysical characterization

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Enzymes were purified using single step nickel affinity chromatography. Secondary structure

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was evaluated using circular dichroism at room temperature. Size exclusion chromatography with

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static light scattering, refractive index, ultraviolet and differential viscometer detectors was used to

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analyze protein quaternary structure, molecular weights, hydrodynamic radius, and intrinsic

136

viscosities. Thermal stability was analyzed by circular dichroism spectroscopy and robotic differential

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scanning calorimetry. The thermal unfolding was monitored by change in the ellipticity or heat

138

capacity over the temperature range 20 to 90 °C. The temperature profile was determined as an effect

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of temperature on enzymatic activity towards 1,3-diiodopropane at pH 8.6 over the temperature range

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5 to 80 °C. The pH profile was determined as an effect of pH on enzymatic activity towards 1,3-

141

dibromopropane at the pH ranging from 4 to 12 at 10, 37 or 55 °C. Substrate specificity towards a set

142

of 30 halogenated compounds was analyzed at 10, 37, or 55 °C. The specific activity data towards 30

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substrates were analyzed by Principal Component Analysis (PCA). The steady-state kinetics of the

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novel HLDs towards 1,2-dibromoethane were measured using an isothermal titration calorimeter at

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either 10, 37, or 55 °C. Enantioselectivity was evaluated from kinetic resolution of 2-bromopentane or

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ethyl 2-bromopropionate at 20 °C. Enzymatic activity towards chemical warfare agent sulfur mustard

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was measured using fluorescent assay. The degradation of a selected environmental pollutants, 1,3-

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dichloropropene, γ-hexachlorocyclohexane, hexabromocyclododecane was analyzed using robotic

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GC-MS. Detailed experimental protocols are described in the Supporting Information section.

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Results

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In silico screening

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The developed automated workflow for the in silico identification and characterization of

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HLDs provides a useful tool for the selection of interesting proteins for experimental characterization. 6 ACS Paragon Plus Environment

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Sequence database searches led to the identification of 5661 sequences representing putative HLDs

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and their close relatives. In order to automatically distinguish between putative HLD sequences and

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sequences of proteins from other families, average-link hierarchical clustering based on pairwise

157

sequence distances was applied. After removing 39 artificial sequences, 953 putative HLDs were

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retained (333 from HLD-I, 295 from HLD-II, 314 from HLD-III, and 11 from HLD-IIIb). On the basis

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of multiple sequence alignment, 117 incomplete and 178 degenerate sequences were excluded from

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the dataset. The substitution of halide-stabilizing residues was the most common reason for exclusion

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(Table S2). The remaining 658 putative HLDs were subjected to homology modelling and in silico

162

characterization. The following data were gathered for each putative HLD: (i) sequence annotations,

163

(ii) the taxonomy of the source organism, (iii) extremophilic properties of the source organism, (iv) a

164

list of highly similar proteins and the most closely related known HLDs, (v) the HLD subfamily, (vi)

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composition of the catalytic pentad, (vii) the domain composition, (viii) the predicted solubility, and if

166

applicable, (ix) suitable template for homology modelling and (x) constructed homology model, (xi)

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the volume and area of the catalytic pocket, (xii) characteristics of access tunnels and (xiii) structures

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of enzyme-substrate complexes.

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The majority of sequences in HLD-I, HLD-II, and HLD-IIIb were correctly annotated (75%,

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80% and 71% respectively), while this was the case for only 26% of the HLD-III sequences (Table

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S3). More than half of the sequences in HLD-III were annotated generally as α/β-hydrolase fold

172

enzymes (45%) or hydrolases (10%). Due to the presence of multi-domain proteins, 3% of the HLD-I

173

sequences and 11% of the HLD-III sequences were annotated as CMP deaminases and acyl-CoA

174

synthetases respectively. Miss-annotations of single-domain proteins were rare (2 proteins). An

175

overview of source organisms, catalytic pentads and domain compositions of the putative HLDs

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identified is provided in Figure 2. The sequences of putative HLDs were identified in the genomes of

177

organisms from all three of the domains of life. The source organisms included 3 thermophilic, 1

178

cryophilic, 13 psychrophilic, 3 psychrophilic-moderate halophilic, 12 moderate halophilic, and 4

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extreme halophilic strains. The majority of the putative HLDs of extremophilic origin were found in

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subfamilies HLD-I and HLD-III. The prevalent compositions of the catalytic pentads agreed with

181

those described previously36. Potential alternative catalytic pentad compositions were predicted for

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26% of HLD-I, 6% of HLD-II and 14% of HLD-IIIb sequences.

183

Even though all HLDs that have been experimentally characterized to date are single-domain

184

proteins, we identified a number of multi-domain proteins in the HLD-I and HLD-III subfamilies. The

185

N-terminal cytidine and deoxycytidylate deaminase domain were detected in 12 HLD-I sequences,

186

while 60 HLD-III sequences had a C-terminal AMP binding domain and one HLD-III sequence had

187

the N-terminal radical SAM domain. N-terminal transmembrane helices were predicted for 6 out of 7

188

HLD-IIIb sequences, while they were present in only a small proportion of sequences from the other

189

three subfamilies. Since the majority of structurally characterized HLDs can be found in the HLD-II

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subfamily, the most reliable homology models could be constructed for members of this subfamily 7 ACS Paragon Plus Environment

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(Figure S1). No protein structures are currently available for members of the HLD-III/b subfamilies,

192

limiting the possibility of homology modelling in these subfamilies (10% for HLD-III and none for

193

HLD-IIIb; Figure S2). Overall, homology models were built and evaluated for 275 sequences.

194

The predicted volumes of catalytic pockets ranged from 126 Å3 to 1981 Å3 (Figure S3).

195

Generally, the HLD-I subfamily members were predicted to have smaller pockets (median volume 554

196

Å3) than HLD-II (716 Å3) and HLD-III (777 Å3). Tunnels were calculated for the ensemble of all

197

superimposed homology models and then clustered, enabling automated and direct comparison of the

198

tunnels identified in different proteins. The three top-ranked tunnel clusters, corresponding to the p1,

199

p2 and p3 tunnels, were further analyzed. Given that the probe radius used was 1 Å, the p1 and p2

200

tunnels were found in the majority of the models analyzed (99% and 84% respectively), while the p3

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tunnel was identified in only 50% of models (Figure S4). Finally, 34 potential HLD substrates were

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docked to homology models and evaluated (Table S4). Generally, the largest number of substrates in

203

the reactive orientation was detected for HLD-II (Figure S5). Almost 15% of HLD-II members were

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found to have more than 5 substrates in the reactive orientation, compared to, respectively, 5% and 4%

205

of the HLD-I and HLD-III subfamily members. One even no substrate was identified for 67% of the

206

HLD-III members, compared to 43% of the HLD-I and 43% of HLD-II members.

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The subsequent semi-rational selection was employed to prioritize the computationally

208

characterized set of 658 putative HLDs based on their sequence and structural characteristics as well

209

as the annotations available. To further enrich the sequence diversity for this fold family, we excluded

210

putative HLDs that had sequence identity lower than 90% to any that had been experimentally

211

characterized. Gathered data for remaining 530 sequentially distinct putative HLDs were compiled

212

into the dataset, on which the selection criteria were applied. The initial criterion was aimed to

213

maximize the diversity of the target properties within HLD family. Further we prioritized the putative

214

HLDs predicted as soluble with high probability, those with lowest identity to known HLDs, or if

215

homology model was available, those predicted as likely active HLDs with high confidence.

216

Simultaneously, we strived to filter out or minimize the candidates from HLDs-III subfamily, since

217

they are often difficult-to-express. This procedure was followed until the required number of hits with

218

the given properties was received as illustrated in Table S5. It enabled sampling of putative HLDs

219

with the most diverse or completely novel properties. The set of 20 selected genes encoding putative

220

HLDs consisted of (i) bacterial, eukaryotic and archaeal enzymes, (ii) single- and multi-domain

221

enzymes, (iii) enzymes originating from extremophilic organisms, (iv) enzymes belonging to four

222

subfamilies, (v) enzymes with alternative composition of the catalytic pentads, (vi) enzymes with

223

small and large active-site cavity, and (vii) enzymes possessing HLD activity with high confidence

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(Table 1, Table S6). Putative HLDs are denoted according to the previously established convention

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(first letter is ‘D’ for dehalogenase; second and third letters are the initials of the source organism; and

226

a last letter ‘A’ or ‘B’ refers to the first or second HLD from a single source organism).

227 8 ACS Paragon Plus Environment

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Figure 2. Overview of putative HLDs identified. Most putative HLD sequences are composed of one

230

α/β-hydrolase domain (single-domain). Additionally, some sequences contain the N-terminal cytidine

231

and deoxycytidylate deaminase domain (CMP/dCMP deaminase), the N-terminal radical SAM domain

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(radical SAM), the C-terminal AMP binding domain (AMP binding) or transmembrane helices (TM).

233

The catalytic pentad in HLDs is composed of nucleophile-catalytic acid-base+halide-stabilizing

234

residues. The nucleophile and catalytic base are conserved in all family members, whereas the

235

catalytic acid and halide-stabilizing residues are variable (highlighted in bold).


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Table 1. Annotations and predicted properties of 20 putative HLDs selected for experimental characterization. Source organism Name DacA DssA

Predicted catalytic pentad

Presence of additional protein domain

IIIb

2 catalytic acids

TM helices

Subfamily Organism

Taxonomy

Aspergillus clavatus NRRL 1

Eukaryota

Extremophile

Shewanella sediminis HAW-EB3

Bacteria

psychrophile

I

3 halide-stabilizing residues

thermophile

DcaA

Chloroflexus aurantiacus J-10-fl

Bacteria

III

standard

DdaA

Desulfatibacillum alkenivorans AK-01

Bacteria

III

standard

DamA

Amycolatopsis mediterranei S699

Bacteria

II

standard

DmtA

Microbacterium testaceum StLB037

Bacteria

III

standard

DtaA

Trichoderma atroviride IMI 206040

Eukaryota

II

standard

DsbA

Streptomyces bingchenggensis BCW-1

Bacteria

DhmeA

Haloferax mediterranei ATCC 33500

Archaea

DadA

Alcanivorax dieselolei B5

DmgA

radical SAM AMP-binding

Volume of active site cavity [Å3] N/A

Radii of transport tunnels p1/p2/p3 [Å] N/A

Number of predicted active compounds N/A

N/A

N/A

N/A

N/A

N/A

N/A

N/A

N/A

N/A

1507

2.1/1.6/1.0

5

N/A

N/A

N/A

348

1.3/1.4/-

8

II

standard

796

2.2/1.3/-

9

III

standard

N/A

N/A

N/A

Bacteria

II

standard

1218

1.5/1.6/-

5

marine gamma proteobacterium HTCC2148

Bacteria

I


N/A

N/A

N/A

DpaB

Paraglaciecola agarilytica NO2

Bacteria

moderate halophile + psychrophile

I

standard

396

1.9/-/-

4

DpaA

Paraglaciecola agarilytica NO2

Bacteria

moderate halophile + psychrophile

I

standard

943

1.9/-/1.4

1

Marinobacter santoriniensis NKSG1

Bacteria

extreme halophile

I

standard

928

1.9/1.2/1.2

3

I


N/A

N/A

N/A

standard

N/A

N/A

N/A

126

1.8/-/-

7

456

2.1/1.1/1.1

7

DmsaA

moderate halophile

DgpA

gamma proteobacterium NOR5-3

Bacteria

DcsA

Caenispirillum salinarum AK4

Bacteria

II

DsxA

Sandarakinorhabdus sp. AAP62

Bacteria

I

standard

I


DlxA DncA DmmaA

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Limnohabitans sp. Rim47

Bacteria

psychrophile

dCMP_cyt_deam

Nonomuraea coxensis

Bacteria

II

standard

1981

2.5/1.6/1.6

1

Mycobacterium marinum str. Europe

Bacteria

II

standard

545

2.1/1.1/1.1

8

Parameters used

as selection criteria are highlighted in grey. N/A – prediction not available due to lack of homology model.

10

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Expression analysis and activity screening

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The expression analysis of putative HLD genes was performed in three different E. coli

241

strains, with two types of cultivation media and under five expression conditions (Figure S6). In total,

242

15 (75%) out of 20 target genes were overexpressed and 12 (60%) genes provided proteins in a soluble

243

form that enabled screening of enzymatic activity. We observed some agreement between the

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theoretically predicted and the experimentally determined solubility of the 12 HLDs that were

245

successfully produced in E. coli (Table S7). A robotic platform employing a 96-well microtiter plate

246

format was set-up for fast screening of the HLD activity. Altogether, the activities of cell-free extracts

247

of 12 soluble putative HLDs were screened against 3 diverse halogenated substrates (1-iodobutane,

248

1,2-dibromoethane, and 4-bromobutyronitrile) in an all-enzyme versus an all-substrate screen format

249

at 3 temperatures regime (10, 37, and 55 °C) to maximize the chance of detecting HLD activity. Out of

250

these 12 soluble HLDs, 9 exhibited hydrolytic activity towards at least one of the substrates tested

251

(Table S8). Eight out of nine novel HLDs were successfully purified and subjected to detailed

252

biochemical and biophysical characterization.

253

Biochemical characterization

254

Biochemical and biophysical characterization included the (i) determination of folding and

255

secondary structure, (ii) quaternary structure, (iii) thermostability, (iv) temperature and pH optima, (v)

256

substrate specificity, (vi) steady-state kinetics, (vii) enantioselectivity, and (viii) activity towards

257

selected environmental pollutants and warfare agent.

258

Circular dichroism spectroscopy was used to assess the correctness of folding and secondary

259

structure composition. All enzymes exhibited CD spectra characteristic of α-helical content and proper

260

folding48 (Figure S7). The quaternary structure was examined by size exclusion chromatography.

261

DpaB, DsxA, DgpA, DtaA, and DsbA are monomeric proteins with calculated molecular weights (Mw)

262

ranging between 31.2 and 36.9 kDa. DpaA is as a dimer with a determined Mw 70.6 kDa and DhmeA

263

is an oligomer with Mw >2 MDa (Table S9). The oligomeric state of DmsaA could not be determined

264

due to protein precipitation under the conditions tested. Thermally induced denaturation of novel

265

HLDs was tested by monitoring ellipticity or heat capacity (Table S10). Three enzymes originating

266

from psychrophilic organisms (DpaA, DpaB, and DgpA) exhibited significantly lower melting

267

temperatures Tm = 35.2 - 38.2 °C in comparison to the enzymes of mesophilic origin with Tm = 47.2 -

268

54.6 °C. The highest melting temperature Tm = 70.6 °C was determined for the archaeal enzyme

269

DhmeA, making this enzyme the most thermostable wild-type HLD ever reported.

270

The temperature and pH profiles were determined using high-throughput robotic assay.

271

Altogether, the novel HLDs exhibited high diversity of operational temperature optima ranging from


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20 to 70 °C, while majority of previously characterized HLDs35 possess narrow range of temperature

273

optima from 30 to 50 °C (Table 2). Moreover, DhmeA showed nearly 90% of its maximum activity

274

even at 70 °C (Figure S8). In correspondence to previously characterised HLDs, the optimal pH

275

conditions ranges between neutral to moderate alkaline condition for most of the novel HLDs variants

276

(Figure S9). Remarkably wide pH tolerance was observed in the case of DhmeA which maintain

277

significant activity in alkaline conditions to nearly pH 11 and DtaA covering unusually broad pH

278

range between 5.7 and 10.0.

279

Substrate specificity was assessed with a panel of thirty halogenated hydrocarbons (Figure

280

S10). All enzymes exhibited a preference for halogenated hydrocarbons in the following order:

281

brominated > iodinated >> chlorinated (Table S11). The optimal length of the alkyl-chain for the

282

substrate was between three and four carbon atoms (Figure 3A). Majority of enzymes possessed rather

283

narrow substrate specificities, converting 12-22 out of the 30 halogenated hydrocarbons. The broadest

284

substrate specificity profile was detected for DtaA, which showed activity towards 27 of the substrates,

285

including the recalcitrant environmental pollutant 1,2,3-trichloropropane. PCA of the transformed data

286

clustered the novel enzymes within substrate specificity groups (SSG) based on their overall substrate

287

specificity profiles (Figure 3C, 3E). The novel HLDs are spread across different SSGs indicating

288

significant diversity. DhmeA and DtaA were clustered in SSG-I, whereas the rest of enzymes in SSG-

289

IV. PCA of untransformed specific activities compared the overall activities of HLDs (Figure 3B).

290

Many of the new enzymes exhibited moderate or low activities, indicating that the natural substrates

291

for the new family members are not adequately covered by the used set of 30 representative

292

compounds. The striking exception is the enzyme DsxA, which showed outstanding activity towards

293

most of the tested substrates. This enzyme exhibited the highest specific activity 493.7, 661.2, and

294

444.6 nmol.s-1.mg-1 towards 1-bromobutane, 1,3-dibromopropane and 1-bromo-3-chloropropane,

295

respectively. This is 2-3 times higher than those recorded for any previously identified HLDs.


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296

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Table 2. Temperature and pH profiles of 8 biochemically characterized HLDs.

297

13


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Page 14 of 24

298 299

Figure 3. Comparison of the substrate specificities and overall catalytic activities of novel HLDs with previously characterized enzymes using

300

multivariate statistics. (A) Substrate specificity profiles of newly discovered HLDs toward 30 halogenated substrates. (B) The score-contribution plot t1 shows

301

differences in overall activities of individual HLDs and explains 40% of the variance in the untransformed dataset. (C) The score plot t1/t2/t3 from PCA of the

302

transformed dataset, which suppressed differences in absolute activities and allowed substrate specificity profiles to be compared. The score plot, which

303

describes 55.5% of the variance in the dataset, shows enzymes clustered in individual substrate-specificity groups (SSGs). Objects (HLDs) with similar

304

properties (specificity profiles) are co-localized. (D+E) The loading plot p1/p2 and the corresponding score plot t1/t2 from PCA of the transformed dataset. The

305

score plot describes 45.0% of the variance in the dataset. The loading plot shows the main substrates for each SSG. Brominated substrates are depicted by

306

amber,

chlorinated

in

green,

iodinated

in

blue

and

brominated

&

chlorinated

in

black. 14


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307

The catalytic properties of the novel enzymes were assessed by measuring steady-state

308

kinetics towards the model substrate 1,2-dibromoethane (Table S12). With the exception of DmsaA,

309

which provided classical hyperbolic kinetics, all novel enzymes exhibited positive cooperativity with

310

Hill coefficients from 1.3 to 2.4. All newly discovered HLDs have shown high K0.5 values with 1,2-

311

dibromoethane (≥ 2.1 mM). The kinetics of DsxA was determined also with 1,3-dibromopropane.

312

Significantly lower K0.5 = 0.17 mM and high kcat = 16.5 .s-1 results in exceptionally high catalytic

313

efficiency (kcat/K0.5 = 96.82 mM-1.s-1), which is approximately 5.5-fold higher in comparison to as the

314

most efficient native HLD of today DadB17DadB.

315

The enantioselectivity of novel HLDs was assayed by determining the kinetic resolution of

316

model β-bromoalkane (2-bromopentane) and model α-bromoester (ethyl 2-bromopropionate). High

317

enantioselectivity (E-value >200) towards ethyl 2-bromopropionate was observed with DpaA, DpaB,

318

DsxA, and DtaA (Figures S11 and S12), moderately enantioselective DmsaA and DhmeA provided

319

E-value 54 and 79, negligible enantioselectivity was showed by DgpA and DsbA (Table S13). In most

320

cases only weak enantioselectivity (E-value < 15) was recorded with 2-bromopentane. The only

321

exception was DpaA, which exhibited moderate enantioselectivity with E-value 85. All enzymes

322

showed (R)- enantiopreference which is in correspondence with previously characterized HLDs22.

323

Degradation of halogenated environmental pollutants and warfare agents is one of the main

324

applications of HLDs (Table S14). The activity of novel HLDs has been tested with 1,3-

325

dichloropropene, hexabromocyclododecane, and γ-hexachlorocyclohexane. All enzymes showed

326

significant catalytic activities towards 1,3-dichloropropene (0.5 – 149.3 nmol.s-1.mg-1) a synthetic

327

compound introduced into the environment through its use as a fumigant. Activity to other tested

328

environmental pollutants has not been detected. Novel enzymes were also screened with the chemical

329

weapon sulfur mustard. Sulfur mustard is a prominent warfare chemical which has been shown to be

330

transformed to the non-toxic product through the action of HLDs28. The screening identified

331

significant activity of DtaA towards sulfur mustard (1.46 nmol.s-1.mg-1), which makes this enzyme a

332

potential candidate for use in decontamination mixtures or biodetection devices.


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333

Page 16 of 24

Discussion

334

In this study, we bring our contribution to the big data challenge in the post-genomics era by

335

the development of an automated in silico screening protocol for the exploitation of the protein

336

functional diversity within an enzyme family. Since the rapidly growing genomic databases may

337

contain vague sequence annotations and miss-annotations, our sequence-based search was employed

338

to identify the new members of a protein family based on their evolutionary relationships to other

339

known family members. The putative HLD sequences were automatically identified using global

340

pairwise sequence identities and average-link hierarchical clustering. Furthermore, we cut the

341

hierarchy of sequences at the level of individual HLD-subfamilies, this minimizing the risk of

342

selecting non-HLD sequences.

343

The sequence analysis identified a number of putative HLDs whose catalytic pentads had

344

alternative compositions: (i) three halide-stabilizing residues, (ii) two catalytic acids, (iii) the HLD-I/II

345

members which have halide-stabilizing Gln/Tyr, (iv) and the HLD-II members with Asp serving as the

346

catalytic acid. It is unclear whether proteins containing these abnormalities represent functional HLDs.

347

Only 58% of the putative HLDs were functionally annotated. While miss-annotations were rare, many

348

proteins were annotated as α/β-hydrolases or hypothetical proteins. The largest number of annotation

349

problems occurred in the HLD-III subfamily, which contains only three experimentally characterized

350

enzymes16,20. All 658 putative HLDs were characterized computationally to provide criteria for

351

candidate selection exploring the diversity within the identified sequence space. The selection

352

procedure was based on the mapping of the sequence and structural characteristics as well as

353

annotations. The procedure yielded candidate proteins originating from new species, environments and

354

under-sampled phyla; proteins with novel domain combinations; proteins with alternative composition

355

of the catalytic pentad; and proteins belonging to newly identified subfamily.

356

To critically evaluate the effectiveness and the main bottlenecks of the platform, we performed

357

the validation of predictions against experimental data. The expression analysis was performed in

358

three different E. coli strains, with two types of cultivation media under five different conditions.

359

Although available solubility prediction tools have been employed during the selection of the

360

candidates and number of diverse expression conditions has been tested, we attained only 60% success

361

rate for the production of soluble proteins. This is in an agreement with previously published large-

362

scale expression trials demonstrating that 50-80% of bacterial proteins and 15-20% of non-bacterial

363

proteins can be produced in E. coli in a soluble form49–51. The production of soluble proteins for

364

experimental characterization remains a challenging, “hit-or-miss” affair, and currently represents the

365

biggest bottleneck in studies of this type. With regard to time requirements and cost effectiveness, a

366

more reasonable strategy is to apply expression screening to a larger number of candidates from

367

protein databases rather than wasting time and resources on optimizing the production of “difficult-to-

368

express” proteins. Robust expression systems must constitute an indispensable component of studies 16 ACS Paragon Plus Environment

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369

of this type50. Prediction of protein solubility using software tools represents attractive future

370

perspective with a challenge towards development of methods achieving higher reliability of

371

estimates.

372

The initial robotic activity screening performed with cell-free extracts revealed 9 active

373

enzymes out of 12 tested, implying 75 % success rate. Lack of activity in the case of 3 enzymes may

374

have been due to low levels of HLD in the cell-free extract, requirements for specific conditions or

375

preferences for unknown substrate. The latter may indicate that the previously identified ‘universal’

376

substrates may not be preferred for all existing HLDs. In order to minimize the risk of missing

377

interesting biocatalysts, the substrates used in the activity screening step should be carefully

378

considered. Thanks to the miscellaneous origins and selection approach oriented to maximize diversity

379

of selected candidates, the identified enzymes exhibited wide range of characteristics with several

380

unique properties. They originated from various phylogenetically unrelated organisms belonging to the

381

domains of Bacteria, Eukaryota, and newly also Archaea. This first archaeal HLD with melting

382

temperature 71 °C represents the most thermostable wild-type HLD known to date. On the contrary,

383

DpaA, DpaB, and DgpA, originating from psychrophilic organisms with melting temperatures below

384

40 °C open possibility for the operation at near-to-zero temperatures, which is attractive mainly for

385

environmental applications, e.g., biodegradation or biosensing35. The eminent diversity of the novel

386

variants with a wide range of optimal temperature from 20 to 70 °C and broad pH range from 6 to 11

387

offers expanding operational window to biotechnological applications. Observed extremophilic

388

characteristics were reliably predicted by in silico protocol.

389

The majority of the newly isolated HLDs exhibited moderate or low enzymatic activities

390

towards 30 halogenated compounds, suggesting that the currently used representative set of substrates

391

for this enzyme family may lack some relevant native substrates. One notable exception is DsxA from

392

Sandarakinorhabdus sp. AAP62, which showed exceptionally high activity towards many brominated

393

substrates, particularly those with alkyl-chains containing 2-4 carbon atoms. This observation

394

corresponds with the restricted volume of the active-site cavity predicted by homology modelling.

395

Importantly, DsxA represents the most catalytically efficient member of this enzyme family ever

396

isolated. Crystallographic and cryo-electron microscopy analysis of several newly isolated HLDs is

397

ongoing in our laboratory. DhmeA from the HLD-III subfamily and DgpA with unique 30 amino acid

398

insertion in the N-terminal part of the cap domain, are particularly interesting targets. Solving the very

399

first structure from subfamily-III will provide a template for predicting the 3D structures of other

400

subfamily members. In subsequent work, we will implement and release the computational part of the

401

workflow as a user friendly web tool. The experimental testing process will be extended by integration

402

of miniaturized lab-on-chip assays, requiring only tiny fractions of a protein material and providing

403

increase in the throughput.


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Page 18 of 24

404

Conclusions

405

In summary, we have demonstrated that the enormous wealth of genomic sequences available

406

in public databases can be efficiently explored by in silico mapping of proteins structural and

407

functional diversity within protein families. Integration of sequence/structural bioinformatics with

408

experimental procedures enabled us to narrow down the number of enzyme candidates under

409

consideration and allowed their catalytic properties to be explored with reasonable expenditures of

410

time and effort. Although examples of sequence-mining platforms have previously been reported, here

411

we describe integrated platform for the computational analysis of the structural and functional

412

diversity of an entire enzyme family, coupled to full biochemical and biophysical characterization of

413

the identified hits10,52. Using our platform, number of novel HLDs with potential practical uses have

414

been identified, characterized and made available to the community in industry and academia. Further

415

application of our platform to other enzyme families will expand our knowledge in the field of

416

enzymology and will lead to the discovery of novel biocatalysts for the biotechnological and

417

pharmaceutical industries.

418

Conflict of interests

419

Dr. Veronika Stepankova, Dr. Radka Chaloupkova and Dr. Zbynek Prokop work part-time at

420

the University biotechnology spin-off company Enantis Ltd. The enzymes isolated throughout this

421

study will be distributed upon request to the community.

422

Supporting Information

423

The Supporting Information is available free of charge on the ACS Publications website. Supporting

424

Methods: In silico screening; Expression analysis; Biochemical and biophysical characterization;

425

Supporting Tables: List of known HLDs used for definition of HLD clusters; Catalytic residues in

426

putative degenerated HLD sequences; Annotations of putative HLD sequences; List of the chemical

427

formulas of 34 halogenated compounds; Overview of the selection process with respective criteria;

428

Accession numbers of putative HLDs; Overview of expression analysis of 20 putative HLDs; Robotic

429

screening of enzymatic activity; The parameters related to size, shape and oligomeric state of HLDs;

430

Melting temperatures of HLDs by CD spectroscopy and robotic DSC; Specific activities of HLDs

431

towards 30 halogenated substrates; Steady-state kinetic parameters of HLDs; Enantioselectivities of

432

HLDs towards 2-bromopentane and ethyl-2-bromopropionate; Activities of HLDs towards warfare

433

agents and environmental pollutants; Supporting Figures: The representative 3D structure of HLD;

434

Availability of homology modelling templates in individual HLD subfamilies; Distributions of

435

predicted volumes of catalytic pockets in HLD subfamilies; Distributions of predicted bottleneck radii

436

of p1, p2 and p3 tunnels in HLD subfamilies; Distributions of mechanism-based geometric criteria for 18 ACS Paragon Plus Environment

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ACS Catalysis

437

reactivity in HLD subfamilies; Expression analysis of the set of 20 putative HLDs; Far-UV circular

438

dichroism spectra of HLDs; Temperature profiles; pH profiles; The set of thirty halogenated

439

substrates; Kinetic resolution of 2-bromopentane; Kinetic resolution of ethyl-2-bromopropionate.

440

Acknowledgments

441

The work was supported by the Grant Agency of the Czech Republic (GA16-06096S, GA16-

442

07965S and GA16-24223S), the Technological Agency of the Czech Republic (TH02010219), the

443

Ministry of Education, Youth, and Sports of the Czech Republic (LQ1605, LO1214) and European

444

Union (720776, 722610). Computational resources were provided by CESNET (LM2015042) and the

445

CERIT Scientific Cloud (LM2015085), as part of the “Projects of Large Research, Development, and

446

Innovations

447

LM2015047, LM2015055).

Infrastructures”

program

(LM2015051,

CZ.02.1.01/0.0/0.0/16_013/0001761,

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Exploration of Enzyme Diversity by Integrating Bioinformatics with

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